Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.
Published in Cell reports (Cambridge) (26.04.2016)
Published in Cell reports (Cambridge) (26.04.2016)
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Journal Article
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
Giannakis, Marios, Mu, Xinmeng Jasmine, Shukla, Sachet A., Qian, Zhi Rong, Cohen, Ofir, Nishihara, Reiko, Bahl, Samira, Cao, Yin, Amin-Mansour, Ali, Yamauchi, Mai, Sukawa, Yasutaka, Stewart, Chip, Rosenberg, Mara, Mima, Kosuke, Inamura, Kentaro, Nosho, Katsuhiko, Nowak, Jonathan A., Lawrence, Michael S., Giovannucci, Edward L., Chan, Andrew T., Ng, Kimmie, Meyerhardt, Jeffrey A., Van Allen, Eliezer M., Getz, Gad, Gabriel, Stacey B., Lander, Eric S., Wu, Catherine J., Fuchs, Charles S., Ogino, Shuji, Garraway, Levi A.
Published in Cell reports (Cambridge) (18.10.2016)
Published in Cell reports (Cambridge) (18.10.2016)
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Journal Article
Avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma: biomarker analysis of the phase 3 JAVELIN Renal 101 trial
Motzer, Robert J., Robbins, Paul B., Powles, Thomas, Albiges, Laurence, Haanen, John B., Larkin, James, Mu, Xinmeng Jasmine, Ching, Keith A., Uemura, Motohide, Pal, Sumanta K., Alekseev, Boris, Gravis, Gwenaelle, Campbell, Matthew T., Penkov, Konstantin, Lee, Jae Lyun, Hariharan, Subramanian, Wang, Xiao, Zhang, Weidong, Wang, Jing, Chudnovsky, Aleksander, di Pietro, Alessandra, Donahue, Amber C., Choueiri, Toni K.
Published in Nature medicine (01.11.2020)
Published in Nature medicine (01.11.2020)
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Journal Article
RNF43 is frequently mutated in colorectal and endometrial cancers
Giannakis, Marios, Hodis, Eran, Jasmine Mu, Xinmeng, Yamauchi, Mai, Rosenbluh, Joseph, Cibulskis, Kristian, Saksena, Gordon, Lawrence, Michael S, Qian, Zhi Rong, Nishihara, Reiko, Van Allen, Eliezer M, Hahn, William C, Gabriel, Stacey B, Lander, Eric S, Getz, Gad, Ogino, Shuji, Fuchs, Charles S, Garraway, Levi A
Published in Nature genetics (01.12.2014)
Published in Nature genetics (01.12.2014)
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Journal Article
Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial
Powles, Thomas, Sridhar, Srikala S., Loriot, Yohann, Bellmunt, Joaquim, Mu, Xinmeng Jasmine, Ching, Keith A., Pu, Jie, Sternberg, Cora N., Petrylak, Daniel P., Tambaro, Rosa, Dourthe, Louis M., Alvarez-Fernandez, Carlos, Aarts, Maureen, di Pietro, Alessandra, Grivas, Petros, Davis, Craig B.
Published in Nature medicine (01.12.2021)
Published in Nature medicine (01.12.2021)
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Journal Article
Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Kan, Zhengyan, Ding, Ying, Kim, Jinho, Jung, Hae Hyun, Chung, Woosung, Lal, Samir, Cho, Soonweng, Fernandez-Banet, Julio, Lee, Se Kyung, Kim, Seok Won, Lee, Jeong Eon, Choi, Yoon-La, Deng, Shibing, Kim, Ji-Yeon, Ahn, Jin Seok, Sha, Ying, Mu, Xinmeng Jasmine, Nam, Jae-Yong, Im, Young-Hyuck, Lee, Soohyeon, Park, Woong-Yang, Nam, Seok Jin, Park, Yeon Hee
Published in Nature communications (30.04.2018)
Published in Nature communications (30.04.2018)
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Journal Article
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
Smith, Aaron M, Walsh, Jonathan R, Long, John, Davis, Craig B, Henstock, Peter, Hodge, Martin R, Maciejewski, Mateusz, Mu, Xinmeng Jasmine, Ra, Stephen, Zhao, Shanrong, Ziemek, Daniel, Fisher, Charles K
Published in BMC bioinformatics (20.03.2020)
Published in BMC bioinformatics (20.03.2020)
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Journal Article
Genomics and privacy: implications of the new reality of closed data for the field
Greenbaum, Dov, Sboner, Andrea, Mu, Xinmeng Jasmine, Gerstein, Mark
Published in PLoS computational biology (01.12.2011)
Published in PLoS computational biology (01.12.2011)
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Journal Article
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes
Montgomery, Stephen B, Goode, David L, Kvikstad, Erika, Albers, Cornelis A, Zhang, Zhengdong D, Mu, Xinmeng Jasmine, Ananda, Guruprasad, Howie, Bryan, Karczewski, Konrad J, Smith, Kevin S, Anaya, Vanessa, Richardson, Rhea, Davis, Joe, MacArthur, Daniel G, Sidow, Arend, Duret, Laurent, Gerstein, Mark, Makova, Kateryna D, Marchini, Jonathan, McVean, Gil, Lunter, Gerton
Published in Genome research (01.05.2013)
Published in Genome research (01.05.2013)
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Journal Article
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer
Fu, Yao, Liu, Zhu, Lou, Shaoke, Bedford, Jason, Mu, Xinmeng Jasmine, Yip, Kevin Y, Khurana, Ekta, Gerstein, Mark
Published in Genome biology (01.01.2014)
Published in Genome biology (01.01.2014)
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Journal Article
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms
Abyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew, Korbel, Jan O., Lam, Hugo Y. K., Lee, Charles, Gerstein, Mark B.
Published in Nature communications (01.06.2015)
Published in Nature communications (01.06.2015)
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Journal Article
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Korbel, Jan O, Gerstein, Mark B, Lam, Hugo Y K, Mu, Xinmeng Jasmine, Stütz, Adrian M, Tanzer, Andrea, Cayting, Philip D, Snyder, Michael, Kim, Philip M
Published in Nature biotechnology (2010)
Published in Nature biotechnology (2010)
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Journal Article
TIME (Tumor Immunity in the MicroEnvironment) classification based on tumor CD274 (PD-L1) expression status and tumor-infiltrating lymphocytes in colorectal carcinomas
Hamada, Tsuyoshi, Soong, Thing Rinda, Masugi, Yohei, Kosumi, Keisuke, Nowak, Jonathan A., da Silva, Annacarolina, Mu, Xinmeng Jasmine, Twombly, Tyler S., Koh, Hideo, Yang, Juhong, Song, Mingyang, Liu, Li, Gu, Mancang, Shi, Yan, Nosho, Katsuhiko, Morikawa, Teppei, Inamura, Kentaro, Shukla, Sachet A., Wu, Catherine J., Garraway, Levi A., Zhang, Xuehong, Wu, Kana, Meyerhardt, Jeffrey A., Chan, Andrew T., Glickman, Jonathan N., Rodig, Scott J., Freeman, Gordon J., Fuchs, Charles S., Nishihara, Reiko, Giannakis, Marios, Ogino, Shuji
Published in Oncoimmunology (03.07.2018)
Published in Oncoimmunology (03.07.2018)
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Journal Article
Interleukin-29 Functions Cooperatively with Interferon to Induce Antiviral Gene Expression and Inhibit Hepatitis C Virus Replication
Pagliaccetti, Nicole E., Eduardo, Roger, Kleinstein, Steven H., Mu, Xinmeng Jasmine, Bandi, Prasanthi, Robek, Michael D.
Published in The Journal of biological chemistry (31.10.2008)
Published in The Journal of biological chemistry (31.10.2008)
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Journal Article
The real cost of sequencing: higher than you think
Sboner, Andrea, Mu, Xinmeng Jasmine, Greenbaum, Dov, Auerbach, Raymond K, Gerstein, Mark B
Published in Genome biology (25.08.2011)
Published in Genome biology (25.08.2011)
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Journal Article
HLA-A03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study
Naranbhai, Vivek, Viard, Mathias, Dean, Michael, Groha, Stefan, Braun, David A, Labaki, Chris, Shukla, Sachet A, Yuki, Yuko, Shah, Parantu, Chin, Kevin, Wind-Rotolo, Megan, Mu, Xinmeng Jasmine, Robbins, Paul B, Gusev, Alexander, Choueiri, Toni K, Gulley, James L, Carrington, Mary
Published in The lancet oncology (01.01.2022)
Published in The lancet oncology (01.01.2022)
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Journal Article
Architecture of the human regulatory network derived from ENCODE data
Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro, Abyzov, Alexej, Addleman, Nick, Bhardwaj, Nitin, Boyle, Alan P., Cayting, Philip, Charos, Alexandra, Chen, David Z., Cheng, Yong, Clarke, Declan, Eastman, Catharine, Euskirchen, Ghia, Frietze, Seth, Fu, Yao, Gertz, Jason, Grubert, Fabian, Harmanci, Arif, Jain, Preti, Kasowski, Maya, Lacroute, Phil, Leng, Jing, Lian, Jin, Monahan, Hannah, O’Geen, Henriette, Ouyang, Zhengqing, Partridge, E. Christopher, Patacsil, Dorrelyn, Pauli, Florencia, Raha, Debasish, Ramirez, Lucia, Reddy, Timothy E., Reed, Brian, Shi, Minyi, Slifer, Teri, Wang, Jing, Wu, Linfeng, Yang, Xinqiong, Yip, Kevin Y., Zilberman-Schapira, Gili, Batzoglou, Serafim, Sidow, Arend, Farnham, Peggy J., Myers, Richard M., Weissman, Sherman M., Snyder, Michael
Published in Nature (London) (06.09.2012)
Published in Nature (London) (06.09.2012)
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Journal Article
Inherited DNA-Repair Defects in Colorectal Cancer
AlDubayan, Saud H., Giannakis, Marios, Moore, Nathanael D., Han, G. Celine, Reardon, Brendan, Hamada, Tsuyoshi, Mu, Xinmeng Jasmine, Nishihara, Reiko, Qian, Zhirong, Liu, Li, Yurgelun, Matthew B., Syngal, Sapna, Garraway, Levi A., Ogino, Shuji, Fuchs, Charles S., Van Allen, Eliezer M.
Published in American journal of human genetics (01.03.2018)
Published in American journal of human genetics (01.03.2018)
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Journal Article
Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Grasso, Catherine S, Giannakis, Marios, Wells, Daniel K, Hamada, Tsuyoshi, Mu, Xinmeng Jasmine, Quist, Michael, Nowak, Jonathan A, Nishihara, Reiko, Qian, Zhi Rong, Inamura, Kentaro, Morikawa, Teppei, Nosho, Katsuhiko, Abril-Rodriguez, Gabriel, Connolly, Charles, Escuin-Ordinas, Helena, Geybels, Milan S, Grady, William M, Hsu, Li, Hu-Lieskovan, Siwen, Huyghe, Jeroen R, Kim, Yeon Joo, Krystofinski, Paige, Leiserson, Mark D M, Montoya, Dennis J, Nadel, Brian B, Pellegrini, Matteo, Pritchard, Colin C, Puig-Saus, Cristina, Quist, Elleanor H, Raphael, Ben J, Salipante, Stephen J, Shin, Daniel Sanghoon, Shinbrot, Eve, Shirts, Brian, Shukla, Sachet, Stanford, Janet L, Sun, Wei, Tsoi, Jennifer, Upfill-Brown, Alexander, Wheeler, David A, Wu, Catherine J, Yu, Ming, Zaidi, Syed H, Zaretsky, Jesse M, Gabriel, Stacey B, Lander, Eric S, Garraway, Levi A, Hudson, Thomas J, Fuchs, Charles S, Ribas, Antoni, Ogino, Shuji, Peters, Ulrike
Published in Cancer discovery (01.06.2018)
Published in Cancer discovery (01.06.2018)
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